4 — Assignment #1
This journal entry will outline my progress while completing assignment 1.
Time estimated: 7 d; taken: 8 d; date started: 2020-01-27; date completed: 2020-02-18
This page had to re-updated after switching datasets
Dataset: GSE136864
Title of the paper:
The ETS transcription factor ELF1 regulates a critical, broadly antiviral program distinct from the type I interferon response.
Context:
ELF1 is a protein found in humans, and expressed by the ELF1 gene. This protein is found primarily in lymphocytes, white blood cells, that provide immune responses to attack foreign objects detected in the body. Usually when a virus enters the body, proteins called interferons are released which inhibit replication of the virus. However it was discovered that through this experiment the ELF1 transcriptional program is distinct from interferons and provides an additional layer to the immune system's response.
Note: Transcription is the first step in gene expression, where DNA is used as a template to form messenger RNA which contain the blueprints for creating polypeptides and other proteins.
Summary of experiment:
- In this experiment, the growth of viral infections and host responses were studied in the presence of the ELF1 gene.
- A549 cells (found in human lung tissue) were either:
- not transduced, or
- transduced with the empty vector
- transduced with ELF1-WT
- transduced with ELF1-R8A mutant
- Indicated cultures were also stimulated under interferon beta for 6hrs and 48 hrs. For example, the image below shows the process after A549 cells were transduced and after 48 hrs, cells were introduced to the influenza A virus. High-content microscopy was then conducted to determine % of virus-infected cells. The image below shows this exact process.
Link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6932815/figure/ppat.1007634.g002/
I was interested in choosing an experiment related to the immune system and its response to viral infections (in the recent news of the corona virus outbreak).
I had to switch between datasets because I realized my data set did not contain counts of RNA seq data. Using the GEO NCBI search engine, it was quite easy to apply filters and search for an alternate dataset that matched my interests.
GEO Accession viewer. (n.d.). Retrieved from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE136864
Transcription: an overview of DNA transcription (article). (n.d.). Retrieved from https://www.khanacademy.org/science/biology/gene-expression-central-dogma/transcription-of-dna-into-rna/a/overview-of-transcription
